DNA Microarray Screening
Microarray screening is typically used for whole-genome transcriptional profiling. An RNA sample is amplified and converted to labeled cRNA, which is hybridized to a high-density array of oligonucleotide probes. Quantification of the signal intensity of the fluorescent label for each probe provides a measurement of transcript abundance. The Core uses Affymetrix GeneChips for transcriptional profiling; 3' expression arrays are available for a variety of organisms. Additional applications include detection of alternative splicing via exon arrays, and analysis of gene regulation via ChIP-chip on tiling arrays.
1. Sample: 5 µg total RNA at 500 ng/µL minimum concentration
- samples that do not meet these standards require additional processing (e.g., two rounds of amplification) by the Core staff; please contact prior to sample submission
2. MIAME sample submission datasheet ( excel form)
3. GeneChip (one per sample)
High-quality RNA is the single most important component of transcriptional profiling. We have obtained excellent results using the Qiagen RNeasy Mini kit for RNA isolation. RNA that is not immediately isolated from sample material should be stabilized by physical (such as freezing in liquid nitrogen) or chemical (RNAlater for tissue samples, or RNAprotect for harvested cells) methods. Follow the manufacturer's protocols for RNA isolation from particular types of samples (e.g., plant material). For RNA isolated using TRIzol reagent, we recommend an additional purification (such as RNeasy Mini) to remove impurities that can impair the labeling reaction.
Microarray data, including QC and statistical metrics analysis, are deposited into a web-accessible Oracle database (EDGE, for Effectual Database for Gene Expression). Researchers at NIDDK have access to data analysis software packages through floating licenses. File formatting for either of these programs can be performed directly via the EDGE web interface.
The cost for microarray screening is $400 per sample. In addition, the user provides the GeneChips for screening; prices effective as of October 2008 are listed here. Please consult with the Core staff prior to ordering to insure that you obtain the correct GeneChip for your experiment.
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Page last updated: May 31, 2009